3dttest

Gosset (Student) t-test sets of 3D datasets

Usage 1: 3dttest [options] -set1 datasets ... -set2 datasets
...

for comparing the
means of 2 sets of datasets (voxel by voxel).

Usage 2: 3dttest [options] -base1 bval -set2 datasets ...

for comparing the mean
of 1 set of datasets against a constant.

OUTPUTS:

A single dataset is
created that is the voxel-by-voxel difference

of the mean of set2
minus the mean of set1 (or minus 'bval').

The output dataset
will be of the intensity+Ttest ('fitt') type.

The t-statistic at
each voxel can be used as an interactive

thresholding tool in
AFNI.

t-TESTING OPTIONS:

-set1 datasets ...
= Specifies the collection of datasets to put into

the first set. The mean of set1 will be tested

with a 2-sample t-test
against the mean of set2.

N.B.: -set1 and -base1 are mutually exclusive!

-base1 bval = 'bval' is a numerical value that the
mean of set2

will be tested against with a 1-sample t-test.

-set2 datasets ...
= Specifies the collection of datasets to put into

the second set. There must be at
least 2 datasets

in each of set1 (if used) and set2.

-paired = Specifies the use of a
paired-sample t-test to

compare set1 and set2. If this
option is used,

set1 and set2 must have the same cardinality.

N.B.: A paired test is intended for use when the set1 and set2

dataset function values may be pairwise correlated.

If they are in fact uncorrelated, this test has less

statistical 'power' than the unpaired (default) t-test.

This loss of power is
the price that is paid for

insurance against pairwise correlations.

-unpooled = Specifies that the variance
estimates for set1 and

set2 be computed separately (not pooled together).

This only makes sense if -paired is NOT given.

N.B.: If this option is used, the number of degrees

of freedom per voxel is a variable, rather

than a constant. NOT
RECOMMENDED.

-workmem mega = 'mega' specifies the number of
megabytes of RAM

to use for statistical workspace.
It defaults

to 12. The program will run
faster if this is

larger (see the NOTES section below).

The -base1 or -set1 command line switches must follow all
other options

(including those described below) except for the -set2
switch.

INPUT EDITING OPTIONS: The same as are available in 3dmerge.

OUTPUT OPTIONS: these options control the output files.

-session dirname
= Write output into given directory (default=./)

-prefix pname
= Use 'pname' for the output directory prefix

(default=tdif)

-datum type
= Use 'type' to store the output difference

in the means; 'type' may be short or float.

How the default is determined is described

in the notes below.

NOTES:

** To economize on
memory, 3dttest makes multiple passes through

the input
datasets. On each pass, the entire
editing process

will be carried
out again. For efficiency's sake, it is

better to carry
out the editing using 3dmerge to produce

temporary datasets, and then run 3dttest on
them. This applies

with particular
force if a 'blurring' option is used.

Note also that
editing a dataset requires that it be read into

memory in its
entirety (so that the disk file is not altered).

This will
increase the memory needs of the program far beyond

the level set
by the -workmem option.

** The input
datasets are specified by their .HEAD files,

but their .BRIK
files must exist also! This program cannot

'warp-on-demand' from other datasets.

** This program
cannot deal with time-dependent or complex-valued datasets!

By default, the
output dataset function values will be shorts if the

first input
dataset is byte- or short-valued; otherwise they will be

floats. This behavior may be overridden using the
-datum option.

However, the
t-statistic at each voxel will be always be

stored as a
short integer that is 1000 times the actual t-value.

INPUT DATASET NAMES

-------------------

This program accepts datasets that are modified on input
according to the

following schemes:

'r1+orig[3..5]' {sub-brick selector}

'r1+orig<100.200>'
{sub-range
selector}

'r1+orig[3..5]<100..200>' {both selectors}

'3dcalc( -a r1+orig
-b r2+orig -expr 0.5*(a+b) )'
{calculation}

For the gruesome details, see the output of 'afni -help'.